arklumpus / treeviewer Goto Github PK

Hi! First of all, great program! Very intuitive and easy to use.

I've had problems adding the Plot alignment module, when I click "select attachment" to get the FASTA alignment, nothing opens allowing me to select a file

PS: Program installed on Windows 10

If I edit my tree, e.g. by changing the node labels from 'length' to 'support', or by editing the font of the leaf labels, and then view the tree as a different style (e.g. changing from rooted to unrooted), all my edits are lost, even after going back to the original style. It would be really helpful if these edited features remained stored, similar to what happens when 'Further transformations' are applied. Thanks for the great tools though!

I want to cite TreeViewer in a manuscript. Is there a citation I should use or just link to the GitHub?

Congrats, you have developed a pretty nice tool! I'm testing it with beast analysis using time stamped viral genomes. I was trying to set the tree scale axis to year and months like I do in Figtree adding the date of the most recent sample, but it looks like TreeViewer is more tunnelled to million years scale. Is that correct?

Are there any way of adding the such scale for time stamped trees and converting automatically the timing to years and months?

Hi,
I just cannot find it - is there a "undo changes" option?

Thank you for the amazing tool! One additional module that could be quite useful would allow users to specify a list of nodes to prune from the tree. Currently, this is sort of implemented, but i) a list cannot be specified (e.g. either by a regex or TXT file) and ii) if a set of nodes is selected, it prunes all the way up to the most recent common ancestor (MRCA). The workaround for issue i) is simple enough, but issue ii) is more challenging to resolve because it means I have to manually prune each node in the list. I understand that pruning up to the MRCA is probably desirably in many cases, but I've encountered many scenarios where I simply want to pluck off a list of nodes, while leaving everything else intact.

Hi,

in TreeViewer_setup.sh (which should be executed with sudo), one of the first steps just after user has had the chance to enter custom installation directory is to clean up said directory with the following command:
rm -rf $prefix/TreeViewer, where $prefix is either "/usr/lib" or whatever was provided by the user.

In case of a mistake, where user made a mistake and accidentally inserted a space, e.g. / home/user/bin instead of /home/user/bin, this clean up would result in script executing rm -rf / home/user/TreeViewer and deletion of the whole root filesystem.

I would suggest at very least modifying clean up command by quoting the input rm -rf "$prefix/TreeViewer", in this case rm would fail with invalid input.

I don't think it's safe to assume that this sort of mistake won't occur (it did to me... good thing I bypassed the sudo requirement).

Lukas

Hello,

I'm trying to open a tree file (output from MCMCTree), but when I try to load it an error box pops up saying "An error has occurred while loading the file! Index was out of range. Must be non-negative and less than the size of the collection. (Parameter 'index')".

I tried exporting it as a nexus file from FigTree and I can open that version of the tree file, but it loses all of the age estimate data in the process. Any ideas how I can get this to load?

Many thanks,
Emily

Hello,
I'm using version 2.1.0 on RockyLinux 9, but I can't get spaces in my leaf labels. I can have underscores, but if I open the same nwk file with the underscores replaced with spaces, the labels are just all squished together with no spaces.

Label Attribute Name is set to "String"

If I click the labels, I can individually edit them to add spaces, but my tree has 75 items and this seems like a bug?

I just installed TreeViewer on macOS and I keep getting "The action "Run Shell Script" encountered an error. Any suggestions on how to to solve this? Thank you!

Hi,

Thanks for creating such an awesome tool!

I have encountered a bug where TreeViewerCommandLine reads lines passed from the command line in reverse.

$ cat plot.txt
open test.tre
Y
$ TreeViewerCommandLine < plot.txt
TreeViewer v1.2.2 (command-line v1.1.1.0)

Type "help" for a list of available commands

Unknown command: ert.tset nepo
Unknown command: Y
>^D
>exit

Strangely enough redirecting the stdout fixes the problem.

$ TreeViewerCommandLine < plot.txt 1> plot.txt.log 
TreeViewer v1.2.2 (command-line v1.1.1.0)

Type "help" for a list of available commands

>open test.tre

  Suggested modules:

    Consensus (32914d41-b182-461e-b7c6-5f0263cc1ccd)
    Radial (95b61284-b870-48b9-b51c-3276f7d89df1)

  Would you like to load the suggested modules? [Y(es)/N(o)] Y

  Options for module Consensus (32914d41-b182-461e-b7c6-5f0263cc1ccd):

    No options available


  Options for module Radial (95b61284-b870-48b9-b51c-3276f7d89df1):

    ┌─────── Tree size ────────┐
    │ #1   Width:    2030      │
    │ #2   Height:    2030     │
    └──────────────────────────┘
    ┌─────── Tree area ────────┐
    │ #3   Start angle:    0   │
    │ #4   Sweep angle:    360 │
    └──────────────────────────┘

>
>^D
>exit

I have tested this on both Mac and Linux systems and the results are the same.

Cheers,
Tim.

Hi there,

I am doing a phylogeny study and would like to use TreeViewer to generate the circular tree for publication, while I met some troubles for the tree file input format. May I ask if this software support the tree generated by MEGA X as input (.mtsx format)? If not, are there any available formats you may recommend?

Best regards,
Chao

Hi! I am trying to use TreeViewer and have a question on color shades on clusters.
Are there any modules that can draw color shades (or big "blocks") onto taxa or monophyletic clades? Which I mean is to draw a rectangular block consisting all of the branches or the names of one clade in a rectangular tree, aiming to emphasize. Sometimes I think it is necessary to draw different colored shades especially for there are a lot of different taxa.
Thank you!

I have a tree (newick format) that I've imported into TreeViewer. Whenever I try to export the tree as PDF or SVG, I get an error:

"Error while saving the SVG file: No attachment selected!"

I'm not sure what to try to get around this. I've never had this issue before and not sure what to do.

Here is the tree.nwk data:
(((((((iscR_protein_Eco_K12_MG1655:0.28290401,Shewanella:0.24067579)0.7540:0.13098450,Pseudomonas_aeruginosa_PAO1:0.19009611)0.9080:0.16061088,(Neisseria:0.44825208,Rhodobacter:0.58663179)0.4000:0.06135371)0.9640:0.34878359,(Cyanobacteria_Microcystis:0.19272268,Cyanobacteria_Synechocystis:0.34394328)0.9980:0.47179395)0.5820:0.22153197,(Deinococcus_radiodurans:0.38238652,(Clostridioides:0.54126126,Bacillus_subtitles:0.48034944)0.4340:0.19611611)0.4580:0.22838653)0.4180:0.16477862,Novosphingobium:0.81610562)0.2080:0.03889063,Streptomyces:0.80658385,(Termotoga:1.20374859,Zymo:1.08310660)0.6040:0.33290562);

Hello!
Is it possible to add circular clade highlights (example: ggtree R package)?

P.S. Unlike other tools, TreeViewer's search and navigation/zoom functionalities are fast!

Hello!

I have been using TreeViewer to plot data on my trees and I have found it very convenient and could create nice visualizations.
However I am running into some issues with my new tree.
I wish to plot data about hosts of some symbionts I am studying on the tips of my phylogeny.
However, it seems that TreeViewer only accounts for the first character in the column of my attribute. Example, I would have the following hosts:

Haliclona
Hyrtrios
Petrosia

TreeViewer would display two colors, one for "H" (the two hosts starting by H) and one for "P". I have thought about assigning a single letter for each of my host but I have more hosts than letters in the alphabet. I have also tried with number but it is the same, eventually TreeViewer would read "2", "21", "29" as the same thing.

I am wondering how to circumvent this!
Thank you for your time.

Hi!
Is it possible to export a tree in a custom zoom (i.e. as shown in screen)?

Thanks in advance.